Try adding Ubuntu stage to publish Docker image

.github/workflows/publish.yml

@@ -18,10 +18,7 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Set up Quarto
-        uses: quarto-dev/quarto-actions/setup@v2
-
-      - name: Deploy on GitHub Pages
+      - name: Publish to GitHub Pages
         uses: quarto-dev/quarto-actions/publish@v2
         with:
           target: gh-pages

env/publish/Dockerfile

@@ -9,7 +9,6 @@ RUN apt-get update \
         ca-certificates \
         curl \
     && apt-get clean
-
 RUN mkdir -p /opt/quarto \
     && curl -o quarto.tar.gz -L "https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-${TARGETARCH}.tar.gz" \
     && tar -zxvf quarto.tar.gz -C /opt/quarto/ --strip-components=1 \
@@ -18,22 +17,27 @@ RUN mkdir -p /opt/quarto \
 #
 # Second stage: Conda environment
 #
-FROM condaforge/miniforge3:24.7.1-0
-LABEL org.opencontainers.image.authors="[email protected]"
-LABEL org.opencontainers.image.description="Dockerfile for the Tools for Reproducible Research NBIS / Elixir workshop"
-COPY --from=quarto /opt/quarto /opt/quarto
-ENV PATH="${PATH}:/opt/quarto/bin"
+FROM condaforge/miniforge3:24.7.1-0 AS conda
 RUN apt-get update \
     && apt-get install -y --no-install-recommends \
         pkg-config \
     && apt-get clean
-
-# Copy and install the Conda environment
 COPY environment.yml ./
 RUN conda config --set channel_priority strict \
     && conda env update --name base --file environment.yml \
     && conda clean --all --force-pkgs-dirs --yes
 
+#
+# Third stage: Final image
+#
+FROM ubuntu:20.04
+COPY --from=quarto /opt/quarto /opt/quarto
+COPY --from=conda /opt/conda /opt/conda/
+ENV PATH="${PATH}:/opt/quarto/bin:/opt/conda/bin"
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+        ca-certificates
+
 # Use bash as shell
 SHELL ["/bin/bash", "-c"]
 
@@ -42,3 +46,6 @@ WORKDIR /work
 
 # Start Bash shell by default
 CMD /bin/bash
+
+LABEL org.opencontainers.image.authors="[email protected]"
+LABEL org.opencontainers.image.description="Dockerfile for the Tools for Reproducible Research NBIS / Elixir workshop"

env/publish/environment.yml

@@ -4,8 +4,7 @@ channels:
 dependencies:
 
   # Command line
-  - gh
-  - jq
+  - git
   - snakemake-minimal
 
   # R